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We are all individuals… bioinformatics in the personalized medicine era

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Abstract

The medical landscape is evolving at a rapid pace, creating the opportunity for more personalized patient treatment and shifting the way healthcare is approached and thought about. With the availability of (epi)genome-wide, transcriptomic and proteogenomic profiling techniques detailed characterization of a disease at the level of the individual is now possible, offering the opportunity for truly tailored approaches for treatment and patient care. While improvements are still expected, the techniques and the basic analytical tools have reached a state that these can be efficiently deployed in both routine research and clinical practice. Still, some major challenges remain. Notably, holistic approaches, integrating data from several sources, e.g. genomic and epigenomic, will increase the understanding of the underlying biological concepts and provide insight into the causes, effects and effective solutions. However, creating and validating such a knowledge base, potentially for different levels of expertise, and integrating several data points into meaningful information is not trivial.

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References

  1. L. Van Neste, G.R. Jones, W. Van Criekinge, J.S. Clark, Personalized Medicine 8, 623 (2011)

  2. H.M. O‘Hagan, W. Wang, S. Sen, C. Destefano Shields, S.S. Lee, Y.W. Zhang, E.G. Clements, Y. Cai, L. Van Neste, H. Easwaran, R.A. Casero, C.L. Sears, S.B. Baylin, Cancer Cell 20, 606 (2011)

    Article  PubMed Central  PubMed  Google Scholar 

  3. J.M. Yi, M. Dhir, L. Van Neste, S.R. Downing, J. Jeschke, S.C. Glöckner, M. de Freitas Calmon, C.M. Hooker, J.M. Funes, C. Boshoff, K.M. Smits, M. van Engeland, M.P. Weijenberg, C.A. Iacobuzio-Donahue, J.G. Herman, K.E. Schuebel, S.B. Baylin, N. Ahuja, Clin. Cancer Res. 17, 1535 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. L.D. Wood, D.W. Parsons, S. Jones, J. Lin, T. Sjöblom, R.J. Leary, D. Shen, S.M. Boca, T. Barber, J. Ptak, N. Silliman, S. Szabo, Z. Dezso, V. Ustyanksky, T. Nikolskaya, Y. Nikolsky, R. Karchin, P.A. Wilson, J.S. Kaminker, Z. Zhang, R. Croshaw, J. Willis, D. Dawson, M. Shipitsin, J.K.V. Willson, S. Sukumar, K. Polyak, B.H. Park, C.L. Pethiyagoda, P.V.K. Pant, D.G. Ballinger, A.B... Sparks, J. Hartigan, D.R. Smith, E. Suh, N. Papadopoulos, P. Buckhaults, S.D. Markowitz, G. Parmigiani, K.W. Kinzler, V.E. Velculescu, B. Vogelstein, Science 318, 1108 (2007)

  5. Cancer Genome Atlas Research Network, Nature 455, 1061 (2008)

    Article  Google Scholar 

  6. P. Gaildrat, S. Krieger, D. Di Giacomo, J. Abdat, F. Révillion, S. Caputo, D. Vaur, E. Jamard, E. Bohers, D. Ledemeney, J.-P. Peyrat, C. Houdayer, E. Rouleau, R. Lidereau, T. Frébourg, A. Hardouin, M. Tosi, A. Martins, J. Med. Genet. 49, 609 (2012)

    Article  CAS  PubMed  Google Scholar 

  7. C. Mattioli, G. Pianigiani, D. De Rocco, A.M.R. Bianco, E. Cappelli, A. Savoia, F. Pagani, Biochim. Biophys. Acta 1842, 1052 (2014)

    Article  CAS  PubMed  Google Scholar 

  8. C.S. Tellez, D.E. Juri, K. Do, A.M. Bernauer, C.L. Thomas, L.A. Damiani, M. Tessema, S. Leng, S.A. Belinsky, Cancer Res. 71, 3087 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  9. K.E. Schuebel, W. Chen, L. Cope, S.C. Glöckner, H. Suzuki, J.M. Yi, T.A. Chan, L. Van Neste, W. Van Criekinge, S. van den Bosch, M. van Engeland, A.H. Ting, K. Jair, W. Yu, M. Toyota, K. Imai, N. Ahuja, J.G. Herman, S.B. Baylin, PLoS Genet. 3, 1709 (2007)

    Article  CAS  PubMed  Google Scholar 

  10. T.A. Chan, S. Glockner, J.M. Yi, W. Chen, L. Van Neste, L. Cope, J.G. Herman, V. Velculescu, K.E. Schuebel, N. Ahuja, S.B. Baylin, PLoS Med. 5, e114 (2008)

    Article  PubMed Central  PubMed  Google Scholar 

  11. Cancer Genome Atlas Network, Nature 487, 330 (2012)

    Article  Google Scholar 

  12. J.G. Kim, H. Takeshima, T. Niwa, E. Rehnberg, Y. Shigematsu, Y. Yoda, S. Yamashita, R. Kushima, T. Maekita, M. Ichinose, H. Katai, W.S. Park, Y.S. Hong, C.H. Park, T. Ushijima, Cancer Lett. 330, 33 (2013)

    Article  CAS  PubMed  Google Scholar 

  13. J.M. Yi, A.A. Guzzetta, V.J. Bailey, S.R. Downing, L. Van Neste, K.B. Chiappinelli, B.P. Keeley, A. Stark, A. Herrera, C. Wolfgang, E.P. Pappou, C.A. Iacobuzio-Donahue, M.G. Goggins, J.G. Herman, T.-H. Wang, S.B. Baylin, N. Ahuja, Clin. Cancer Res. 19, 6544 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. L. Van Neste, J.G. Herman, G. Otto, J.W. Bigley, J.I. Epstein, W. Van Criekinge, Prostate 72, 1248 (2012)

    Article  PubMed  Google Scholar 

  15. J. Jeschke, L. Van Neste, S.C. Glöckner, M. Dhir, M.F. Calmon, V. Deregowski, W. Van Criekinge, I. Vlassenbroeck, A. Koch, T.A. Chan, L. Cope, C.M. Hooker, K.E. Schuebel, E. Gabrielson, A. Winterpacht, S.B. Baylin, J.G. Herman, N. Ahuja, Epigenetics 7, 701 (2012)

    Article  CAS  PubMed  Google Scholar 

  16. J.G. Herman, S.B. Baylin, N. Engl, J. Med. 349, 2042 (2003)

    CAS  Google Scholar 

  17. K. Mensaert, S. Denil, G. Trooskens, W. Van Criekinge, O. Thas, T. De Meyer, Environ. Mol. Mutagen. 55, 155 (2014)

    Article  CAS  PubMed  Google Scholar 

  18. L. Van Neste, J.G. Herman, W. Van Criekinge, TJOP, 1, 29 (2013)

  19. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, G.G. Sutton, H.O. Smith, M. Yandell, C.A. Evans, R.A. Holt, J.D. Gocayne, P. Amanatides, R.M. Ballew, D.H. Huson, J.R. Wortman, Q. Zhang, C.D. Kodira, X.H. Zheng, L. Chen, M. Skupski, G. Subramanian, P.D. Thomas, J. Zhang, G.L. Gabor Miklos, C. Nelson, S. Broder, A.G. Clark, J. Nadeau, V.A. McKusick, N. Zinder, A.J. Levine, R.J. Roberts, M. Simon, C. Slayman, M. Hunkapiller, R. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, K. Biddick, V. Bonazzi, R. Brandon, M. Cargill, I. Chandramouliswaran, R. Charlab, K. Chaturvedi, Z. Deng, V. Di Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A.E. Gabrielian, W. Gan, W. Ge, F. Gong, Z. Gu, P. Guan, T.J. Heiman, M.E. Higgins, R.R. Ji, Z. Ke, K.A. Ketchum, Z. Lai, Y. Lei, Z. Li, J. Li, Y. Liang, X. Lin, F. Lu, G.V. Merkulov, N. Milshina, H.M. Moore, A.K. Naik, V.A. Narayan, B. Neelam, D. Nusskern, D.B. Rusch, S. Salzberg, W. Shao, B. Shue, J. Sun, Z. Wang, A. Wang, X. Wang, J. Wang, M. Wei, R. Wides, C. Xiao, C. Yan, A. Yao, J. Ye, M. Zhan, W. Zhang, H. Zhang, Q. Zhao, L. Zheng, F. Zhong, W. Zhong, S. Zhu, S. Zhao, D. Gilbert, S. Baumhueter, G. Spier, C. Carter, A. Cravchik, T. Woodage, F. Ali, H. An, A. Awe, D. Baldwin, H. Baden, M. Barnstead, I. Barrow, K. Beeson, D. Busam, A. Carver, A. Center, M.L. Cheng, L. Curry, S. Danaher, L. Davenport, R. Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, N. Garg, A. Gluecksmann, B. Hart, J. Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, J. Johnson, F. Kalush, L. Kline, S. Koduru, A. Love, F. Mann, D. May, S. McCawley, T. McIntosh, I. McMullen, M. Moy, L. Moy, B. Murphy, K. Nelson, C. Pfannkoch, E. Pratts, V. Puri, H. Qureshi, M. Reardon, R. Rodriguez, Y.H. Rogers, D. Romblad, B. Ruhfel, R. Scott, C. Sitter, M. Smallwood, E. Stewart, R. Strong, E. Suh, R. Thomas, N.N. Tint, S. Tse, C. Vech, G. Wang, J. Wetter, S. Williams, M. Williams, S. Windsor, E. Winn-Deen, K. Wolfe, J. Zaveri, K. Zaveri, J.F. Abril, R. Guigó, M.J. Campbell, K.V. Sjolander, B. Karlak, A. Kejariwal, H. Mi, B. Lazareva, T. Hatton, A. Narechania, K. Diemer, A. Muruganujan, N. Guo, S. Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, S. Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, M. Caminha, J. Carnes-Stine, P. Caulk, Y.H. Chiang, M. Coyne, C. Dahlke, A. Mays, M. Dombroski, M. Donnelly, D. Ely, S. Esparham, C. Fosler, H. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, B. Gropman, M. Harris, J. Heil, S. Henderson, J. Hoover, D. Jennings, C. Jordan, J. Jordan, J. Kasha, L. Kagan, C. Kraft, A. Levitsky, M. Lewis, X. Liu, J. Lopez, D. Ma, W. Majoros, J. McDaniel, S. Murphy, M. Newman, T. Nguyen, N. Nguyen, M. Nodell, S. Pan, J. Peck, M. Peterson, W. Rowe, R. Sanders, J. Scott, M. Simpson, T. Smith, A. Sprague, T. Stockwell, R. Turner, E. Vent, M. Wanger, M. Wen, D. Wu, M. Wu, A. Xia, A. Zandieh, X. Zhu, Science 291, 1304 (2001)

    Article  CAS  PubMed  Google Scholar 

  20. E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, J. Baldwin, K. Devon, K. Dewar, M. Doyle, W. FitzHugh, R. Funke, D. Gage, K. Harris, A. Heaford, J. Howland, L. Kann, J. Lehoczky, R. LeVine, P. McEwan, K. McKernan, J. Meldrim, J.P. Mesirov, C. Miranda, W. Morris, J. Naylor, C. Raymond, M. Rosetti, R. Santos, A. Sheridan, C. Sougnez, N. Stange-Thomann, N. Stojanovic, A. Subramanian, D. Wyman, J. Rogers, J. Sulston, R. Ainscough, S. Beck, D. Bentley, J. Burton, C. Clee, N. Carter, A. Coulson, R. Deadman, P. Deloukas, A. Dunham, I. Dunham, R. Durbin, L. French, D. Grafham, S. Gregory, T. Hubbard, S. Humphray, A. Hunt, M. Jones, C. Lloyd, A. McMurray, L. Matthews, S. Mercer, S. Milne, J.C. Mullikin, A. Mungall, R. Plumb, M. Ross, R. Shownkeen, S. Sims, R.H. Waterston, R.K. Wilson, L.W. Hillier, J.D. McPherson, M.A. Marra, E.R. Mardis, L.A. Fulton, A.T. Chinwalla, K.H. Pepin, W.R. Gish, S.L. Chissoe, M.C. Wendl, K.D. Delehaunty, T.L. Miner, A. Delehaunty, J.B. Kramer, L.L. Cook, R.S. Fulton, D.L. Johnson, P.J. Minx, S.W. Clifton, T. Hawkins, E. Branscomb, P. Predki, P. Richardson, S. Wenning, T. Slezak, N. Doggett, J.F. Cheng, A. Olsen, S. Lucas, C. Elkin, E. Uberbacher, M. Frazier, R.A. Gibbs, D.M. Muzny, S.E. Scherer, J.B. Bouck, E.J. Sodergren, K.C. Worley, C.M. Rives, J.H. Gorrell, M.L. Metzker, S.L. Naylor, R.S. Kucherlapati, D.L. Nelson, G.M. Weinstock, Y. Sakaki, A. Fujiyama, M. Hattori, T. Yada, A. Toyoda, T. Itoh, C. Kawagoe, H. Watanabe, Y. Totoki, T. Taylor, J. Weissenbach, R. Heilig, W. Saurin, F. Artiguenave, P. Brottier, T. Bruls, E. Pelletier, C. Robert, P. Wincker, D.R. Smith, L. Doucette-Stamm, M. Rubenfield, K. Weinstock, H.M. Lee, J. Dubois, A. Rosenthal, M. Platzer, G. Nyakatura, S. Taudien, A. Rump, H. Yang, J. Yu, J. Wang, G. Huang, J. Gu, L. Hood, L. Rowen, A. Madan, S. Qin, R.W. Davis, N.A. Federspiel, A.P. Abola, M.J. Proctor, R.M. Myers, J. Schmutz, M. Dickson, J. Grimwood, D.R. Cox, M.V. Olson, R. Kaul, N. Shimizu, K. Kawasaki, S. Minoshima, G.A. Evans, M. Athanasiou, R. Schultz, B.A. Roe, F. Chen, H. Pan, J. Ramser, H. Lehrach, R. Reinhardt, W.R. McCombie, M. de la Bastide, N. Dedhia, H. Blöcker, K. Hornischer, G. Nordsiek, R. Agarwala, L. Aravind, J.A. Bailey, A. Bateman, S. Batzoglou, E. Birney, P. Bork, D.G. Brown, C.B. Burge, L. Cerutti, H.C. Chen, D. Church, M. Clamp, R.R. Copley, T. Doerks, S.R. Eddy, E.E. Eichler, T.S. Furey, J. Galagan, J.G. Gilbert, C. Harmon, Y. Hayashizaki, D. Haussler, H. Hermjakob, K. Hokamp, W. Jang, L.S. Johnson, T.A. Jones, S. Kasif, A. Kaspryzk, S. Kennedy, W.J. Kent, P. Kitts, E.V. Koonin, I. Korf, D. Kulp, D. Lancet, T.M. Lowe, A. McLysaght, T. Mikkelsen, J.V. Moran, N. Mulder, V.J. Pollara, C.P. Ponting, G. Schuler, J. Schultz, G. Slater, A.F. Smit, E. Stupka, J. Szustakowski, D. Thierry-Mieg, J. Thierry-Mieg, L. Wagner, J. Wallis, R. Wheeler, A. Williams, Y.I. Wolf, K.H. Wolfe, S.P. Yang, R.F. Yeh, F. Collins, M.S. Guyer, J. Peterson, A. Felsenfeld, K.A. Wetterstrand, A. Patrinos, M.J. Morgan, P. de Jong, J.J. Catanese, K. Osoegawa, H. Shizuya, S. Choi, Y.J. Chen, J. Szustakowki, International human genome sequencing consortium. Nature 409, 860 (2001)

    Article  CAS  PubMed  Google Scholar 

  21. R. Li, C. Yu, Y. Li, T.-W. Lam, S.-M. Yiu, K. Kristiansen, J. Wang, Bioinformatics 25, 1966 (2009)

    Article  CAS  PubMed  Google Scholar 

  22. B. Langmead, S.L. Salzberg, Nat. Methods 9, 357 (2012)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. F. Krueger, S.R. Andrews, Bioinformatics 27, 1571 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. W. Guo, P. Fiziev, W. Yan, S. Cokus, X. Sun, M. Q. Zhang, P.-Y. Chen,M. Pellegrini, BMC Genomics 14, (2013)

  25. T. Sjöblom, S. Jones, L.D. Wood, D.W. Parsons, J. Lin, T.D. Barber, D. Mandelker, R.J. Leary, J. Ptak, N. Silliman, S. Szabo, P. Buckhaults, C. Farrell, P. Meeh, S.D. Markowitz, J. Willis, D. Dawson, J.K.V. Willson, A.F. Gazdar, J. Hartigan, L. Wu, C. Liu, G. Parmigiani, B.H. Park, K.E. Bachman, N. Papadopoulos, B. Vogelstein, K.W. Kinzler, V.E. Velculescu, Science 314, 268 (2006)

    Article  PubMed  Google Scholar 

  26. C.J. Allegra, J.M. Jessup, M.R. Somerfield, S.R. Hamilton, E.H. Hammond, D.F. Hayes, P.K. McAllister, R.F. Morton, R.L. Schilsky, J. Clin. Oncol. 27, 2091 (2009)

    Article  PubMed  Google Scholar 

  27. M.S. Greenblatt, P.O. Chappuis, J.P. Bond, N. Hamel, W.D. Foulkes, Cancer Res. 61, 4092 (2001)

    CAS  PubMed  Google Scholar 

  28. D. Cappellen, C. De Oliveira, D. Ricol, S. de Medina, J. Bourdin, X. Sastre-Garau, D. Chopin, J.P. Thiery, F. Radvanyi, Nat. Genet. 23, 18 (1999)

    CAS  PubMed  Google Scholar 

  29. B.W. van Rhijn, I. Lurkin, F. Radvanyi, W.J. Kirkels, T.H. van der Kwast, E.C. Zwarthoff, Cancer Res. 61, 1265 (2001)

    PubMed  Google Scholar 

  30. H.A. Al-Ahmadie, G. Iyer, M. Janakiraman, O. Lin, A. Heguy, S.K. Tickoo, S.W. Fine, A. Gopalan, Y.-B. Chen, A. Balar, J. Riches, B. Bochner, G. Dalbagni, D.F. Bajorin, V.E. Reuter, M.I. Milowsky, D.B. Solit, J. Pathol. 224, 270 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  31. P. Stephens, S. Edkins, H. Davies, C. Greenman, C. Cox, C. Hunter, G. Bignell, J. Teague, R. Smith, C. Stevens, S. O‘Meara, A. Parker, P. Tarpey, T. Avis, A. Barthorpe, L. Brackenbury, G. Buck, A. Butler, J. Clements, J. Cole, E. Dicks, K. Edwards, S. Forbes, M. Gorton, K. Gray, K. Halliday, R. Harrison, K. Hills, J. Hinton, D. Jones, V. Kosmidou, R. Laman, R. Lugg, A. Menzies, J. Perry, R. Petty, K. Raine, R. Shepherd, A. Small, H. Solomon, Y. Stephens, C. Tofts, J. Varian, A. Webb, S. West, S. Widaa, A. Yates, F. Brasseur, C.S. Cooper, A.M. Flanagan, A. Green, M. Knowles, S.Y. Leung, L.H.J. Looijenga, B. Malkowicz, M.A. Pierotti, B. Teh, S.T. Yuen, A.G. Nicholson, S. Lakhani, D.F. Easton, B.L. Weber, M.R. Stratton, P.A. Futreal, R. Wooster, Nat. Genet. 37, 590 (2005)

    Article  CAS  PubMed  Google Scholar 

  32. P. Hackman, S.M. Hou, F. Nyberg, G. Pershagen, B. Lambert, Mutat. Res. 468, 45 (2000)

    Article  CAS  PubMed  Google Scholar 

  33. E. Greenberg, G. Rechavi, N. Amariglio, O. Solomon, J. Schachter, G. Markel, E. Eyal, PLoS ONE 6, e27400 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. C. Tomasetti, B. Vogelstein, G. Parmigiani, Proc. Natl. Acad. Sci. U. S. A. 110, 1999 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. J. Ye, A. Pavlicek, E.A. Lunney, P.A. Rejto, C.-H. Teng, BMC Bioinforma. 11, 11 (2010)

    Article  Google Scholar 

  36. A.K. Fielding, Blood 116, 3409 (2010)

    Article  CAS  PubMed  Google Scholar 

  37. L.J.M. Mekenkamp, J.C. Haan, D. Israeli, H.F.B. van Essen, J.R. Dijkstra, P. van Cleef, C.J.A. Punt, G.A. Meijer, I.D. Nagtegaal, B. Ylstra, PLoS ONE 9, e86833 (2014)

    Article  PubMed Central  PubMed  Google Scholar 

  38. S.J. Smeets, U. Harjes, W.N. van Wieringen, D. Sie, R.H. Brakenhoff, G.A. Meijer, B. Ylstra, Clin. Cancer Res. 17, 4959 (2011)

    Article  CAS  PubMed  Google Scholar 

  39. A.C. Wolff, M.E.H. Hammond, D.G. Hicks, M. Dowsett, L.M. McShane, K.H. Allison, D.C. Allred, J.M.S. Bartlett, M. Bilous, P. Fitzgibbons, W. Hanna, R.B. Jenkins, P.B. Mangu, S. Paik, E.A. Perez, M.F. Press, P.A. Spears, G.H. Vance, G. Viale, D.F. Hayes, American society of clinical oncology, college of american pathologists. J. Clin. Oncol. 31, 3997 (2013)

    Article  PubMed  Google Scholar 

  40. M. Esteller, J. Garcia-Foncillas, E. Andion, S.N. Goodman, O.F. Hidalgo, V. Vanaclocha, S.B. Baylin, J.G. Herman, N. Engl, J. Med. 343, 1350 (2000)

    CAS  Google Scholar 

  41. M. Esteller, S.R. Hamilton, P.C. Burger, S.B. Baylin, J.G. Herman, Cancer Res. 59, 793 (1999)

    CAS  PubMed  Google Scholar 

  42. M.E. Hegi, A.-C. Diserens, T. Gorlia, M.-F. Hamou, N. de Tribolet, M. Weller, J.M. Kros, J.A. Hainfellner, W. Mason, L. Mariani, J.E.C. Bromberg, P. Hau, R.O. Mirimanoff, J.G. Cairncross, R.C. Janzer, R. Stupp, N. Engl, J. Med. 352, 997 (2005)

    CAS  Google Scholar 

  43. I.J.H. van Vlodrop, H.E.C. Niessen, S. Derks, M.M.L.L. Baldewijns, W. Van Criekinge, J.G. Herman, M. van Engeland, Clin. Cancer Res. 17, 4225 (2011)

    Article  PubMed  Google Scholar 

  44. J.G. Herman, J.R. Graff, S. Myöhänen, B.D. Nelkin, S.B. Baylin, Proc. Natl. Acad. Sci. U. S. A. 93, 9821 (1996)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. I. Vlassenbroeck, S. Califice, A.-C. Diserens, E. Migliavacca, J. Straub, I. Di Stefano, F. Moreau, M.-F. Hamou, I. Renard, M. Delorenzi, B. Flamion, J. DiGuiseppi, K. Bierau, M.E. Hegi, J. Mol. Diagn. 10, 332 (2008)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. J.C. Rice, K.S. Massey-Brown, B.W. Futscher, Oncogene 17, 1807 (1998)

    Article  CAS  PubMed  Google Scholar 

  47. T. Hansmann, G. Pliushch, M. Leubner, P. Kroll, D. Endt, A. Gehrig, S. Preisler-Adams, P. Wieacker, T. Haaf, Hum. Mol. Genet. 21, 4669 (2012)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. A. Meissner, A. Gnirke, G.W. Bell, B. Ramsahoye, E.S. Lander, R. Jaenisch, Nucleic Acids Res. 33, 5868 (2005)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. D. Serre, B.H. Lee, A.H. Ting, Nucleic Acids Res. 38, 391 (2010)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  50. T. De Meyer, E. Mampaey, M. Vlemmix, S. Denil, G. Trooskens, J.-P. Renard, S. De Keulenaer, P. Dehan, G. Menschaert, W. Van Criekinge, PLoS ONE 8, e59068 (2013)

    Article  PubMed Central  PubMed  Google Scholar 

  51. B.P. Berman, D.J. Weisenberger, J.F. Aman, T. Hinoue, Z. Ramjan, Y. Liu, H. Noushmehr, C.P.E. Lange, C.M. van Dijk, R.A.E.M. Tollenaar, D. Van Den Berg, P.W. Laird, Nat. Genet. 44, 40 (2012)

    Article  PubMed Central  CAS  Google Scholar 

  52. M. Sultan, M.H. Schulz, H. Richard, A. Magen, A. Klingenhoff, M. Scherf, M. Seifert, T. Borodina, A. Soldatov, D. Parkhomchuk, D. Schmidt, S. O‘Keeffe, S. Haas, M. Vingron, H. Lehrach, M.-L. Yaspo, Science 321, 956 (2008)

    Article  CAS  PubMed  Google Scholar 

  53. 1000 Genomes Project Consortium, G.R. Abecasis, D. Altshuler, A. Auton, L.D. Brooks, R.M. Durbin, R.A. Gibbs, M.E. Hurles, G.A. McVean, Nature 467, 1061 (2010)

    Article  Google Scholar 

  54. G. Menschaert, W. Van Criekinge, T. Notelaers, A. Koch, J. Crappé, K. Gevaert, P. Van Damme, Mol. Cell. Proteomics 12, 1780 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. P. Flicek, M.R. Amode, D. Barrell, K. Beal, K. Billis, S. Brent, D. Carvalho-Silva, P. Clapham, G. Coates, S. Fitzgerald, L. Gil, C.G. Giron, L. Gordon, T. Hourlier, S. Hunt, N. Johnson, T. Juettemann, A.K. Kaehaeri, S. Keenan, E. Kulesha, F.J. Martin, T. Maurel, W.M. McLaren, D.N. Murphy, R. Nag, B. Overduin, M. Pignatelli, B. Pritchard, E. Pritchard, H.S. Riat, M. Ruffier, D. Sheppard, K. Taylor, A. Thormann, S.J. Trevanion, A. Vullo, S.P. Wilder, M. Wilson, A. Zadissa, B.L. Aken, E. Birney, F. Cunningham, J. Harrow, J. Herrero, T.J.P. Hubbard, R. Kinsella, M. Muffato, A. Parker, G. Spudich, A. Yates, D.R. Zerbino, S.M.J. Searle, Nucleic Acids Res. 42, D749 (2014)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  56. R.M. Kuhn, D. Haussler, W.J. Kent, Brief. Bioinforma. 14, 144 (2013)

    Article  CAS  Google Scholar 

  57. J. Goecks, A. Nekrutenko, J. Taylor, G. Team, Genome Biol. 11, (2010)

  58. J. Wrangle, E.O. Machida, L. Danilova, A. Hulbert, N. Franco, W. Zhang, S.C. Glöckner, M. Tessema, L. Van Neste, H. Easwaran, K.E. Schuebel, J. Licchesi, C.M. Hooker, N. Ahuja, J. Amano, S.A. Belinsky, S.B. Baylin, J.G. Herman, M.V. Brock, Clin. Cancer Res. 20, 1856 (2014)

    Article  CAS  PubMed  Google Scholar 

  59. D.L. Wheeler, D.M. Church, A.E. Lash, D.D. Leipe, T.L. Madden, J.U. Pontius, G.D. Schuler, L.M. Schriml, T.A. Tatusova, L. Wagner, B.A. Rapp, Nucleic Acids Res. 29, 11 (2001)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  60. A. Brazma, H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca-Serra, S.-A. Sansone, Nucleic Acids Res. 31, 68 (2003)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  61. A. Brazma, P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, M. Vingron, Nat. Genet. 29, 365 (2001)

    Article  CAS  PubMed  Google Scholar 

  62. R. Leinonen, H. Sugawara, M. Shumway, International nucleotide sequence database collaboration. Nucleic Acids Res. 39, D19 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, D. Haussler, Genome Res. 12, 996 (2002)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  64. T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik, M. Clamp, Nucleic Acids Res. 30, 38 (2002)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  65. Nat. Methods 5, 989 (2008)

  66. N.R. Wray, J. Yang, B.J. Hayes, A.L. Price, M.E. Goddard, P.M. Visscher, Nat. Rev. Genet. 14, 507 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  67. N.R. Wray, M.E. Goddard, P.M. Visscher, Genome Res. 17, 1520 (2007)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  68. M.F. Fraga, E. Ballestar, M.F. Paz, S. Ropero, F. Setien, M.L. Ballestar, D. Heine-Suñer, J.C. Cigudosa, M. Urioste, J. Benitez, M. Boix-Chornet, A. Sanchez-Aguilera, C. Ling, E. Carlsson, P. Poulsen, A. Vaag, Z. Stephan, T.D. Spector, Y.-Z. Wu, C. Plass, M. Esteller, Proc. Natl. Acad. Sci. U. S. A. 102, 10604 (2005)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  69. P. Poulsen, M. Esteller, A. Vaag, M.F. Fraga, Pediatr. Res. 61, 38R (2007)

    Article  PubMed  Google Scholar 

  70. International Human Genome Sequencing Consortium, Nature 431, 931 (2004)

    Article  Google Scholar 

  71. A.H.C. Wong, I.I. Gottesman, A. Petronis, Hum. Mol. Genet. 14(Spec No 1), R11 (2005)

    Article  CAS  PubMed  Google Scholar 

  72. R. Yoshida, M. Nakajima, Y. Watanabe, J.-T. Kwon, T. Yokoi, Br. J. Clin. Pharmacol. 54, 511 (2002)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  73. C. Rodríguez-Antona, M. Niemi, J.T. Backman, L.I. Kajosaari, P.J. Neuvonen, M. Robledo, M. Ingelman-Sundberg, Pharmacogenomics J. 8, 268 (2008)

    Article  PubMed  Google Scholar 

  74. M. Wadelius, L.Y. Chen, J.D. Lindh, N. Eriksson, M.J.R. Ghori, S. Bumpstead, L. Holm, R. McGinnis, A. Rane, P. Deloukas, Blood 113, 784 (2009)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  75. J. de Leon, M.T. Susce, R.-M. Pan, M. Fairchild, W.H. Koch, P.J. Wedlund, J. Clin. Psychiatry 66, 15 (2005)

    Article  PubMed  Google Scholar 

  76. L. Pierret, N.V. Baren, A. Bonehill, J. Corthals, A.M.T. Van Nuffel, C. Heirman, T. Roelandt, A. De Coninck, I.V. Riet, E. Degreef, A. Goossens, G. Verfaillie, D. Roseeuw, K. Thielemans, B. Neyns, Melanoma Res. 19, 385 (2009)

    Article  PubMed  Google Scholar 

  77. A. Bonehill, A.M.T. Van Nuffel, J. Corthals, S. Tuyaerts, C. Heirman, V. François, D. Colau, P. van der Bruggen, B. Neyns, K. Thielemans, Clin. Cancer Res. 15, 3366 (2009)

    Article  CAS  PubMed  Google Scholar 

  78. F. Ulloa-Montoya, J. Louahed, B. Dizier, O. Gruselle, B. Spiessens, F.F. Lehmann, S. Suciu, W.H.J. Kruit, A.M.M. Eggermont, J. Vansteenkiste, V.G. Brichard, J. Clin. Oncol. 31, 2388 (2013)

    Article  CAS  PubMed  Google Scholar 

  79. M. Rajasagi, S. A. Shukla, E. F. Fritsch, D. B. Keskin, D. DeLuca, E. Carmona, W. Zhang, C. Sougnez, K. Cibulskis, J. Sidney, K. Stevenson, J. Ritz, D. Neuberg, V. Brusic, S. Gabriel, E. S. Lander, G. Getz, N. Hacohen, and C. J. Wu, Blood (2014)

  80. S. Schwartz, I. Friedberg, I.V. Ivanov, L.A. Davidson, J.S. Goldsby, D.B. Dahl, D. Herman, M. Wang, S.M. Donovan, R.S. Chapkin, Genome Biol. 13, r32 (2012)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  81. P. Lepage, M.C. Leclerc, M. Joossens, S. Mondot, H.M. Blottière, J. Raes, D. Ehrlich, J. Doré, Gut 62, 146 (2013)

    Article  PubMed  Google Scholar 

  82. M. C. Cénit, V. Matzaraki, E. F. Tigchelaar, and A. Zhernakova, Biochim. Biophys. Acta (2014)

  83. J. Jeschke, H.M. O‘Hagan, W. Zhang, R. Vatapalli, M.F. Calmon, L. Danilova, C. Nelkenbrecher, L. Van Neste, I.T.G.W. Bijsmans, M. van Engeland, E. Gabrielson, K.E. Schuebel, A. Winterpacht, S.B. Baylin, J.G. Herman, N. Ahuja, Clin. Cancer Res. 19, 3201 (2013)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  84. G.D. Stewart, L. Van Neste, P. Delvenne, P. Delrée, A. Delga, S.A. McNeill, M. O‘Donnell, J. Clark, W. Van Criekinge, J. Bigley, D.J. Harrison, J. Urol. 189, 1110 (2013)

    Article  PubMed  Google Scholar 

  85. A. W. Partin, L. Van Neste, E. A. Klein, L. S. Marks, J. R. Gee, D. A. Troyer, K. Rieger-Christ, J. S. Jones, C. Magi-Galluzzi, L. A. Mangold, B. J. Trock, R. S. Lance, J. W. Bigley, W. Van Criekinge, and J. I. Epstein, J. Urol. (2014)

  86. S.C. Glöckner, M. Dhir, J.M. Yi, K.E. McGarvey, L. Van Neste, J. Louwagie, T.A. Chan, W. Kleeberger, A.P. de Bruïne, K.M. Smits, C.A.J. Khalid-de Bakker, D.M.A.E. Jonkers, R.W. Stockbrügger, G.A. Meijer, F.A. Oort, C. Iacobuzio-Donahue, K. Bierau, J.G. Herman, S.B. Baylin, M. van Engeland, K.E. Schuebel, N. Ahuja, Cancer Res. 69, 4691 (2009)

    Article  PubMed Central  PubMed  Google Scholar 

  87. V. Melotte, M.H.F.M. Lentjes, S.M. van den Bosch, D.M.E.I. Hellebrekers, J.P.J. de Hoon, K.A.D. Wouters, K.L.J. Daenen, I.E.J.M. Partouns-Hendriks, F. Stessels, J. Louwagie, K.M. Smits, M.P. Weijenberg, S. Sanduleanu, C.A.J. Khalid-de Bakker, F.A. Oort, G.A. Meijer, D.M.A.E. Jonkers, J.G. Herman, A.P. de Bruïne, M. van Engeland, J. Natl. Cancer Inst. 101, 916 (2009)

    Article  CAS  PubMed  Google Scholar 

  88. T.F. Imperiale, D.F. Ransohoff, S.H. Itzkowitz, T.R. Levin, P. Lavin, G.P. Lidgard, D.A. Ahlquist, B.M. Berger, N. Engl, J. Med. 370, 1287 (2014)

    CAS  Google Scholar 

  89. C. Bettegowda, M. Sausen, R.J. Leary, I. Kinde, Y. Wang, N. Agrawal, B.R. Bartlett, H. Wang, B. Luber, R.M. Alani, E.S. Antonarakis, N.S. Azad, A. Bardelli, H. Brem, J.L. Cameron, C.C. Lee, L.A. Fecher, G.L. Gallia, P. Gibbs, D. Le, R.L. Giuntoli, M. Goggins, M.D. Hogarty, M. Holdhoff, S.-M. Hong, Y. Jiao, H.H. Juhl, J.J. Kim, G. Siravegna, D.A. Laheru, C. Lauricella, M. Lim, E.J. Lipson, S.K.N. Marie, G.J. Netto, K.S. Oliner, A. Olivi, L. Olsson, G.J. Riggins, A. Sartore-Bianchi, K. Schmidt, L.-M. Shih, S.M. Oba-Shinjo, S. Siena, D. Theodorescu, J. Tie, T.T. Harkins, S. Veronese, T.-L. Wang, J.D. Weingart, C.L. Wolfgang, L.D. Wood, D. Xing, R.H. Hruban, J. Wu, P.J. Allen, C.M. Schmidt, M.A. Choti, V.E. Velculescu, K.W. Kinzler, B. Vogelstein, N. Papadopoulos, L.A. Diaz, Sci. Transl. Med. 6, 224ra24 (2014)

    Article  PubMed Central  PubMed  Google Scholar 

  90. J. Wrangle, W. Wang, A. Koch, H. Easwaran, H.P. Mohammad, F. Vendetti, W. Vancriekinge, T. Demeyer, Z. Du, P. Parsana, K. Rodgers, R.-W. Yen, C.A. Zahnow, J.M. Taube, J.R. Brahmer, S.S. Tykodi, K. Easton, R.D. Carvajal, P.A. Jones, P.W. Laird, D.J. Weisenberger, S. Tsai, R.A. Juergens, S.L. Topalian, C.M. Rudin, M.V. Brock, D. Pardoll, S.B. Baylin, Oncotarget 4, 2067 (2013)

    PubMed Central  PubMed  Google Scholar 

  91. R.A. Juergens, J. Wrangle, F.P. Vendetti, S.C. Murphy, M. Zhao, B. Coleman, R. Sebree, K. Rodgers, C.M. Hooker, N. Franco, B. Lee, S. Tsai, I.E. Delgado, M.A. Rudek, S.A. Belinsky, J.G. Herman, S.B. Baylin, M.V. Brock, C.M. Rudin, Cancer Discov. 1, 598 (2011)

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  92. M.L. de Groote, P.J. Verschure, M.G. Rots, Nucleic Acids Res. 40, 10596 (2012)

    Article  PubMed Central  PubMed  Google Scholar 

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Van Neste, L., Van Criekinge, W. We are all individuals… bioinformatics in the personalized medicine era. Cell Oncol. 38, 29–37 (2015). https://doi.org/10.1007/s13402-014-0195-3

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